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A Reference Linkage Map for Eucalyptus Hudson et al. BMC Genomics 2012, 13:240 http://www.biomedcentral.com/1471-2164/13/240 RESEARCH ARTICLE Open Access A reference linkage map for Eucalyptus Corey J Hudson1*, Jules S Freeman1,2, Anand RK Kullan3, César D Petroli4, Carolina P Sansaloni4, Andrzej Kilian5, Frank Detering5, Dario Grattapaglia6, Brad M Potts1, Alexander A Myburg3 and René E Vaillancourt1 Abstract Background: Genetic linkage maps are invaluable resources in plant research. They provide a key tool for many genetic applications including: mapping quantitative trait loci (QTL); comparative mapping; identifying unlinked (i.e. independent) DNA markers for fingerprinting, population genetics and phylogenetics; assisting genome sequence assembly; relating physical and recombination distances along the genome and map-based cloning of genes. Eucalypts are the dominant tree species in most Australian ecosystems and of economic importance globally as plantation trees. The genome sequence of E. grandis has recently been released providing unprecedented opportunities for genetic and genomic research in the genus. A robust reference linkage map containing sequence-based molecular markers is needed to capitalise on this resource. Several high density linkage maps have recently been constructed for the main commercial forestry species in the genus (E. grandis, E. urophylla and E. globulus) using sequenced Diversity Arrays Technology (DArT) and microsatellite markers. To provide a single reference linkage map for eucalypts a composite map was produced through the integration of data from seven independent mapping experiments (1950 individuals) using a marker-merging method. Results: The composite map totalled 1107 cM and contained 4101 markers; comprising 3880 DArT, 213 microsatellite and eight candidate genes. Eighty-one DArT markers were mapped to two or more linkage groups, resulting in the 4101 markers being mapped to 4191 map positions. Approximately 13% of DArT markers mapped to identical map positions, thus the composite map contained 3634 unique loci at an average interval of 0.31 cM. Conclusion: The composite map represents the most saturated linkage map yet produced in Eucalyptus. As the majority of DArT markers contained on the map have been sequenced, the map provides a direct link to the E. grandis genome sequence and will serve as an important reference for progressing eucalypt research. Background their value to genetics research has led to numerous link- Genetic linkage maps are valuable resources which can be age mapping projects being undertaken in plants. Detailed used to provide a framework for many genomic analyses. linkage maps have been produced for all of the world’s Linkage maps can be used to investigate the organisation staple cereal species [12], and in forest trees, linkage maps and evolution of genomes through comparative mapping have been produced for many of the most widely-planted [1-3] and serve as a basis for investigating phenotypic species due to their commercial importance as wood and traits of ecological and economic importance through the fibre crops [1,13,14]. localisation of quantitative trait loci [QTL; 4-6]. Subse- Grattapaglia and Sederoff [15] published the first gen- quently, QTL results may be used to help guide the selec- etic linkage map in the forest tree genus Eucalyptus in tion of candidate genes for association studies or be 1994. Subsequently, many mapping pedigrees have been applied in marker-assisted breeding programmes [7,8]. established for the purpose of linkage map construction Linkage maps can also be used to anchor physical maps and associated QTL analyses. More than 20 eucalypt and assist in the assembly of genome sequences [9-11]. genetic linkage maps have been reported with most The wide application of linkage maps in combination with being produced in the main commercially grown species, or their hybrids, from the Eucalyptus subgenus Symphyo- myrtus. Thus, the majority of linkage mapping projects * Correspondence: [email protected] 1School of Plant Science and CRC for Forestry, University of Tasmania, Private have focussed on E. grandis, E. urophylla and E. globulus Bag 55 Hobart, Tasmania 7001, Australia [reviewed in 16], while a smaller number of maps have Full list of author information is available at the end of the article © 2012 Hudson et al., licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Hudson et al. BMC Genomics 2012, 13:240 Page 2 of 11 http://www.biomedcentral.com/1471-2164/13/240 also been produced for E. nitens [17], E. teriticornis effects; 38] and are more useful in some genetic ana- [18,19], E. camaldulensis [20] and for species in the lyses, such as estimating population genetic parameters closely related genus Corymbia [21]. (e.g. inbreeding levels), relative to dominant marker Many early eucalypt linkage maps were constructed types such as DArT. In addition, the DArT marker assay using random amplification of polymorphic DNA can be subject to cross-hybridization from duplicated (RAPD) and amplified fragment length polymorphism loci in the genome, although most such artifacts can be (AFLP) molecular markers [16,22]. However, the an- excluded by preselecting markers exhibiting Mendelian onymous nature of these dominant markers has limited segregation ratios in mapping pedigrees. the transfer of linkage information between studies At present, DArT markers have been used to construct [16,23]. More informative, codominant markers such as linkage maps in seven independent E. globulus and/or isozyme and random fragment length polymorphism E. grandis × E. urophylla hybrid family mapping pedi- (RFLPs) have also been used in eucalypt linkage map- grees [11,32,33]. All of these maps also contain a variable ping, although, their low throughput, low inter-pedigree number of co-dominant microsatellite markers, which polymorphism and labour intensive genotyping require- provide important links to many earlier eucalypt linkage ments have limited their use [16,23]. The more recent maps. In the two largest mapping pedigrees (more than development of highly polymorphic microsatellite mar- 500 individuals each), 1010 [32] and 2229 [33] DArT kers made available a large potential suite of markers markers, were mapped at sub-centiMorgan marker that are transferrable between species and polymorphic densities and collectively more than 4000 DArT and in multiple pedigrees. This enabled linkage group syn- microsatellite markers have been mapped in the seven teny to be established between maps containing com- pedigrees. mon microsatellite markers and the positions and All DArT marker based linkage maps were constructed stability of QTL across multiple species to be examined using the program JoinMap 4.0 [37]. This program is one [e.g. 24-27]. The ability to establish linkage group syn- of the most commonly used linkage mapping programs teny has also enabled moderate-density comparative and appears to be the only software available for building mapping studies [23,28]. linkage maps using the combined segregation data from Recent advances in molecular methods have led to multiple populations [39-41]. However, it is presently not high-throughput genotyping systems being developed feasible to combine the segregation data contained within [e.g. 29,30]. These have made it possible to quickly gen- the seven eucalypt mapping families describe above (col- erate many hundreds of markers in single mapping pedi- lectively 1950 individuals), and successfully order such grees and have helped facilitate the construction of high large numbers of markers within linkage groups (up density linkage maps [12]. Most recently in Eucalyptus, to ~ 500) due to computational limitations (Van Ooijen Diversity Arrays Technology [DArT; 31] has been used pers comm.). To circumvent the limitations of traditional to generate large numbers of molecular markers for gen- segregation-based methods of linkage map construction, etic linkage mapping in several mapping pedigrees alternative marker-merging strategies have been devel- [e.g. 11,32,33]. The eucalypt DArT markers are highly oped. A so-called ‘composite map’ can be produced in transferable across species from subgenus Symphyomyr- which markers from individual component maps are tus [34] and the high-throughput array-based genotyping merged into a single map based on their position relative system provides wide genome coverage [35]. A key bene- to common anchor loci. For example, the ‘neighbours’ fit of the Eucalyptus DArT markers is the public avail- marker-merging approach of Cone et al. [42] and the ability of the sequences of most of the 7680 markers marker-merging method implemented in the PhenoMap contained on the genotyping array [GenBank accession program (GeneFlow Inc. USA) have been used to success- numbers HR865291 - HR872186], thus making it pos- fully construct high density composite maps containing sible to anchor DArT markers directly to the reference several thousand markers in a number of plant species; in- E. grandis genome sequence [v1.0 released January 2011; cluding Sorghum [43], barley [41,44,45] and maize [42,46]. 36]. However, while the DArT technology offers many In this study, a marker-merging method was used to advantages, the DArT markers do suffer some limita- construct a high-density DArT and microsatellite
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